'deprotonate' originates from Modern English, formed from the prefix 'de-' and the verb 'protonate', where 'de-' meant 'remove' and 'protonate' derives from 'proton' + '-ate' used in chemical nomenclature.

'proton' comes from Greek 'protos' meaning 'first'; chemical usage produced 'proton' in Modern English, from which 'protonate' was formed and later 'deprotonate' was coined in chemical contexts in the 19th–20th century.

Initially formed to mean 'to remove or add a proton' in chemical nomenclature contexts; 'deprotonate' specifically came to mean 'to remove a proton' and has retained that specific technical meaning.